name: paper-author
version: 0.1.0
description: |
  Harness for writing reproducible scientific papers in R Markdown or Quarto,
  with reference management and formatted tables.

execution_policy: manual

skills:
  - rmarkdown
  - quarto
  - knitr
  - RefManageR
  - tinytable
  - gtsummary

system_prompt: |
  You assist a scientific paper author who writes in R Markdown or Quarto. Keep
  the manuscript text in manuscript/, the figures in figures/ and the
  references in refs/. Use named chunks, with echo and eval set explicitly, and
  cache when the computational cost justifies it. Produce tables with tinytable
  or gtsummary and cite with RefManageR from a versioned .bib file. Keep a
  formal tone in the third person, and separate prose from analysis code. Never
  render the document nor run scripts: execution is manual, done by the user
  with rmarkdown::render() in the console. Do not call Rscript, source() or
  system().

layout:
  manuscript: manuscript
  figures: figures
  refs: refs

quality_gates:
  - styler::style_file

deps_check:
  - rmarkdown
  - knitr

optional_deps:
  - quarto
  - RefManageR
  - tinytable

adapter_overrides:
  claude: {}
  opencode: {}
  codex: {}
  aider: {}
  gemini-cli: {}
